All Classes

Class	Description
AbstractFastqCollector	The abstract class define commons methods for the Collectors which treats fastq files.
AbstractFastQCSampleTest	This class define an abstract FastQC test.
AbstractGlobalTest	This class define a abstract Global test.
AbstractIlluminaDemuxDataProcessor	This class define an abstract Illumina demultiplexing data processor.
AbstractLaneTest	This class define a abstract Lane test.
AbstractPooledSampleTest	This class define a abstract Global test.
AbstractProjectTest	This class define a abstract Global test.
AbstractQCModuleAozan	This class replace normal class AbstracQCModule form
AbstractSampleSheetConverter	This abstract class define a converter between a samplesheet in XLS format to CSV.
AbstractSampleTest	This class define a abstract sample test.
AbstractSimpleGlobalTest	This class define a simple global test.
AbstractSimpleLaneTest	This class define a simple lane test.
AbstractSimpleProjectTest	This class define a simple lane test.
AbstractSimpleSampleTest	This class define a simple lane test.
AbstractSimpleSampleTest	This class define a simple sample test.
Action	This interface define an action.
ActionService	This class define a service to retrieve an Action.
Aozan2Compatibility	This utility class contains methods for Aozan 2 code source compatibility.
Aozan2Logger
Aozan2QCDataProcessor	This class define an Aozan 2 QC data processor.
Aozan3Exception	This class define an Aozan exception
Aozan3Logger
AozanCollector
AozanException	A nestable Aozan exception.
AozanLock	This class define a global lock for Aozan.
AozanLoggerFactory	This class define a factory for loggers.
AozanRuntimeException	A nestable Aozan runtime exception.
AozanTest	This interface define an Aozan QC test.
AozanTestRegistry	This class define a registry for Aozan tests.
BasecallingModelSelector	This class allow to select the model to use with Dorado from parameters like flowcell or kit references.
BaseCountGlobalTest	This class define a base count global test.
BasePFMeanQualityScoreSampleTest	This class define a percent quality mean score sample test.
Bcl2FastqIlluminaDemuxDataProcessor	This class define an Illumina demultiplexing data processor that use bcl-convert.
Bcl2FastqOutput	This class define the output of bcl2fastq.
Bcl2FastqOutput.Bcl2FastqVersion	This enum defined the versions of bcl2fastq.
BclConvertIlluminaDemuxDataProcessor	This class define an Illumina demultiplexing data processor that use bcl-convert.
BlastContaminantHit	This class define a Blast contiminant Hit.
CategoryDataTypeFilter	This class define a DataTypeFilter that require a specific DataType.
ClusterDensityGlobalTest	The class define test to compute the density cluster mean for the run.
ClusterDensityLaneTest	This class define a lane test on cluster density.
ClusterDensityPFGlobalTest	The class define test to compute the density cluster mean passing filtre for the run.
ClusterDensityPFLaneTest	This class define a lane test on cluster density.
ClusterRecoveryReportSampleTest	The class adds in the qc report html a link to the report recoverable cluster results for each sample.
Collector	This interface define a Collector.
CollectorConfiguration	This class define the configuration of a collector.
CollectorRegistry	This class define a registry for Collectors.
Common	This class define common methods for CLI.
Common	This class contains common methods like logger initialization.
Configuration	This class define a configuration
ConfigurationDefaults	This class contains Configuration object defaults
ConfigurationXMLParser	This class define a XML parser for configuration.
ContaminantFinder	Source FastQC version 0.10.0, not modify.
CopyAndMergeGuppyOutput	Merge FASTQ files from a directory in another directory.
CSVLineParser	This class define a line entry of a CSV file.
CVSParser	This class allow to parse CSV files
Cycle100ErrorRateLaneTest	This class define a test on error rate on 100 cycle.
Cycle20IntensityPercentLaneTest	This class define a test on percent of intensity at cycle 20.
Cycle35ErrorRateLaneTest	This class define a test on error rate on 35 cycle.
Cycle75ErrorRateLaneTest	This class define a test on error rate on 75 cycle.
CycleCountGlobalTest	This class define a cycle count global test.
DataLocation	This class define a data location
DataLocation.Format	Format of the data location
DataProcessor	This interface defines a data processor
DataProcessor.ProcessResult	This interface define a process result
DataProcessorService	This class define a service to retrieve a DataProcessor
DataProcessorTemplateEmailMessage	This class define a template email message for end of step messages.
DataStorage	This class define a data storage.
DataStorageRegistry	This class define a registry for data storages.
DataType	This class define a data type
DataType.Category	Run data type.
DataType.SequencingTechnology	Sequencing technology
DataTypeFilter	This interface define a filter for DataType.
DefaultRunIdGenerator	This class define the default implementation of the RunIsGenerator interface.
DemultiplexingCollector
DemultiplexStatsCollector	This collector parse Demultiplex_Stats.csv file generated by bcl-convert.
DensityLaneTest	This class define a density lane test.
DiscoverNewIlluminaRunDataProcessor	This class define an Illumina run discovering data processor.
DiskUtils	This class contains some system utility methods.
DoradoAction	This class define an "dorado" action that will launch Dorado.
DoradoONTBasecallingDataProcessor	This class implements a Dorado data processor.
DoubleInterval	This class define a double interval.
EmailMessage	This class define define an email message.
EmptyRunConfigurationProvider	This class define an empty run configuration provider
EmptyRunDataProvider	This class define an empty run data provider.
EndIlluminaRunDataProcessor	This class define an Illumina end run data processor.
EntityStat	The class define a entity statistics which compute data collected on project, sample or others and update run data.
ErrorMetricsCollector	This class collects run data by reading the ErrorMetricsOut.bin in InterOp directory.
ErrorRateGlobalTest	The class define test to compute the mean on the error rate phix for the run.
ErrorRateLaneTest	This class define a test on error rate.
ExecAction	This class define an exec action.
ExternalTool	This class define a class for calling external tool in DataProcessors.
ExtractionMetricsCollector	This class collects run data by reading the ExtractionMetricsOut.bin in InterOp directory.
FastQCAdapterContentSampleTest	This class define a sample test for FastQC per tile sequence quality module.
FastQCBasicStatsSampleTest	This class define a sample test for FastQC basic stats module.
FastQCCollector	This class define a FastQC Collector.
FastQCDuplicationLevelSampleTest	This class define a sample test for FastQC duplication level module.
FastQCKmerContentSampleTest	This class define a sample test for FastQC kmer content module.
FastQCNContentSampleTest	This class define a sample test for FastQC N content module.
FastQCOverrepresentedSequencesSampleTest	This class define a sample test for FastQC over represented seqs module.
FastQCPerBaseQualityScoresSampleTest	This class define a sample test for FastQC per base quality score module.
FastQCPerBaseSequenceContentSampleTest	This class define a sample test for FastQC per base sequence content module.
FastQCPerSequenceGCContentSampleTest	This class define a sample test for FastQC basic stats module.
FastQCPerSequenceQualityScoresSampleTest	This class define a sample test for FastQC per sequence quality scores module.
FastQCPerTileSequenceQualitySampleTest	This class define a sample test for FastQC per tile sequence quality module.
FastQCSequenceLengthDistributionSampleTest	This class define a sample test for FastQC sequence length distribution module.
FastqSample	The class correspond of one entity to treat by AbstractFastqCollector, so a sample per lane and in mode-paired one FastSample for each read (R1 and R2).
FastqSampleUtils
FastqScreen	This class execute fastqscreen pair-end mode or single-end.
FastqScreenCollector	This class manages the execution of Fastq Screen for a full run according to the properties defined in the configuration file Aozan, which define the list of references genomes.
FastqScreenGenomes	This class read the alias genome file.
FastQScreenMappedExceptRefGenomeSampleTest	The class adds in the qc report html one result from fastqScreen for each sample.
FastQScreenMappedExceptRefPercentPooledSampleTest	The class adds in the qc report html one result from fastqScreen for each sample, after compile replicat data.
FastQScreenMappedPercentPooledSampleTest	The class add in the qc report html values from FastqScreen for each sample, after compile replica data and for each reference genomes.
FastQScreenMappedPercentSampleTest	The class add in the qc report html values from FastqScreen for each sample and for each reference genomes.
FastqScreenProjectReport	The class set a project HTML report file on detection contamination by compilation report on samples.
FastqScreenPseudoMapReduce	This class account reads that map to each of the reference genome.
FastQScreenReportPooledSampleTest
FastQScreenReportProjectTest
FastQScreenReportSampleTest	The class adds in the qc report html a link to the report fastqScreen for each sample.
FastqScreenResult	This class manages results from fastqscreen.
FastqScreenSAMParser	This class ensures alignment fastqScreen treating the output format BAM of mapper.
FastQScreenSampleOvercontaminationCountPooledSampleTest	The class define test on samples count on a project which exceed a contaminant threshold on percent mapped reads on dataset contaminants genomes.
FastQScreenSampleOvercontaminationCountProjectTest	The class define test on samples count on a project which exceed a contaminant threshold on percent mapped reads on dataset contaminants genomes.
FileUtils	This class defines useful method to handle files.
FirstCycleIntensityLaneTest	This class define a test on first cycle intensity.
GenomeAliases	This class define a storage for genome name aliases.
GenomeNamesPooledSampleTest	The Class GenomesProjectTest.
GenomeNamesProjectTest	The Class GenomesProjectTest.
GenomeNamesSampleTest	This class define a test to get the genome(s) reference(s) of a sample.
Globals	This class contains Globals constants.
Globals	This class contains Globals constants.
GlobalStatsCollector	This class define a Collector for global statistics of the run.
GlobalTest	This interface define a test on lane.
GuppyAction	This class define an guppy action that will launch Guppy.
GuppyONTBasecallingDataProcessor	This class implements a Guppy data processor.
IlluminaProcessedRunDataProvider	This class define a processed data provider for Illumina runs.
IlluminaRawRunDataProvider	This class define a processed data provider for Illumina runs.
IlluminaRunIdWrapper	This class allow to get information from Illumina run id.
IlluminaSampleSheetConverter	This class define a converter between an Illumina samplesheet in XLS format to CSV.
IlluminaSamplesheetRunConfigurationProvider	Get the run configuration from an Illumina samplesheet.
IlluminaSyncDataProcessor	This class define an Illumina synchronization data processor.
IlluminaUtils	This class contents some utility methods for Illumina.
IndexGenerator	This class allow to generate index file like for Aozan 1.x and 2.x.
InLanePercentSampleTest	This class define a sample percent in lane test.
InProjectPercentPooledSampleTest	The class define test to compute the percent reads passing filter on all samples replica in run.
InputData	This class define InputData for processors.
InRunPercentPooledSampleTest	The class define test to compute the percent reads passing filter on all samples replica in run.
Interval	This interface define an interval.
IsIndexedPooledSampleTest	The Class IsIndexedProjectTest.
IsIndexedProjectTest	The Class IsIndexedProjectTest.
JSONUtils	This class contains some utility methods for JSON serialization.
LaneCountGlobalTest	This class define a lane count global test.
LaneCountPooledSampleTest	The Class LanesRunProjectTest.
LaneCountProjectTest	The Class LanesRunProjectTest.
LaneTest	This interface define a test on lane.
LegacyAction	This class define an legacy action.
LegacyRecipes	This class define recipes that perform like Aozan 2 steps.
ListAction	This class define an action that list existing recipes.
LoadingConcentrationPercentGlobalTest	This class define a loading concentration percent global test.
LongInterval	This class define a long interval.
Main	This class define the main class.
MathUtils	This class contains useful math methods.
MaxPFClusterCountPooledSampleTest	The class define a test the maximum on passing filter clusters on samples in a project.
MaxPFClusterCountProjectTest	The class define a test the maximum on passing filter clusters on samples in a project.
MaxRawClusterCountPooledSampleTest	The class define a test the maximum on raw clusters on samples in a project.
MaxRawClusterCountProjectTest	The class define a test the maximum on raw clusters on samples in a project.
MeanPFClusterCountGlobalTest	This class define a raw cluster mean global test.
MeanPhiXRawClusterCountGlobalTest	This class define a raw cluster phix mean global test.
MeanRawClusterCountGlobalTest	This class define a raw cluster global test.
MedianPFClusterCountGlobalTest	This class define a raw cluster mediane global test.
MedianPhiXRawClusterCountGlobalTest	This class define a raw cluster phix mediane global test.
MedianRawClusterCountGlobalTest	This class define a raw cluster mediane global test.
MinPFClusterCountPooledSampleTest	The class define a test the minimum on passing filter clusters on samples in a project.
MinPFClusterCountProjectTest	The class define a test the minimum on passing filter clusters on samples in a project.
MinRawClusterCountPooledSampleTest	The class define a test the minimum on raw clusters on samples in a project.
MinRawClusterCountProjectTest	The class define a test the minimum on raw clusters on samples in a project.
MultiDataTypeFilter	This class define a filter that combine several other filters.
MultiQCCollector	This class define a MultiQC collector.
MultiQCReportProjectTest	This class define a test that allow access to the MultiQC report of a project.
NanoporeSampleSheetConverter	This class define a converter between a Nanopore samplesheet in XLS format to CSV.
NonIndexedBaseCountGlobalTest	This class define a non indexed base count global test.
OccupancyPercentGlobalTest	This class define an occupancy percent global test.
OccupancyPercentLaneTest	This class define an occupancy percent lane test.
OverrepresentedSequencesBlast	This class launches blastn on one sequence query and parses xml result file to identify the best hit.
ParserUtils	This class contains Utility methods to parse XML documents.
PartialDataTypeFilter	This class define a DataTypeFilter that require partial or not DataType.
PFBaseMeanQualityScorePooledSampleTest	The class define test to compute the percent reads passing filter on all samples replica in run.
PFClusterCountGlobalTest	This class define a Passing Filter cluster global test.
PFClusterCountLaneTest	This class define a Passing Filter cluster lane test.
PFClusterCountPooledSampleTest	The class define a test the sum on passing filter clusters on samples in a project.
PFClusterCountProjectTest	The class define a test the sum on passing filter clusters on samples in a project.
PFClusterCountSampleTest	This class define a passing filter clusters count test for samples.
PFClusterPercentGlobalTest	This class define a percent passing filter clusters global test.
PFClusterPercentLaneTest	This class a test on passing filter cluster in a lane.
PFClusterRecoveryCountPooledSampleTest	The class define a test the maximum on raw clusters on samples in a project.
PFClusterSDGlobalTest	This class define a raw cluster standard deviation global test.
PFPercentPooledSampleTest	The class define test to compute the percent reads passing filter on all samples replica in run.
PFPercentSampleTest	This class define a percent passing filter sample test.
PhasingPrephasingPercentLaneTest	This class define a lane test on phasing / prephasing.
PhiXAlignPercentGlobalTest	This class define a lane test on PhiX percent aligned.
PhiXAlignPercentLaneTest	This class define a lane test on PhiX percent aligned.
PhiXRawClusterCountGlobalTest	This class define a raw cluster phix count global test.
PhiXRawClusterCountLaneTest	This class define a lane test on PhiX raw cluster count.
PhiXRawClusterSDGlobalTest	This class define a raw cluster phix standard deviation global test.
PooledSampleTest	This interface define a test on a pooled sample.
PrimaryAnalysisMetricsCollector	This collector collect data from the PrimaryAnalysisMetrics.csv file if exists.
ProjectCountGlobalTest	This class define a projects count global test.
ProjectStatisticsCollector	The class define a statistic collector on project's data to build a project summary table in qc report.
ProjectTest	This interface define a test on lane.
Q30PercentGlobalTest	This class define a Q30 percent global test.
Q30PercentLaneTest	This class define a Q30 percent lane test.
Q30PercentPooledSampleTest	The class define test to compute the percent reads passing filter on all samples replica in run.
Q30PercentSampleTest	This class define a percent Q30 sample test.
QC	This class is the main QC class.
QCReport	This class generate the QC Report.
QCReportExporter	This class export the QC Report in several formats.
QualityMetricsCollector	This class collects run data by reading the QualityMetricsOut.bin in InterOp directory.
RawClusterCountGlobalTest	This class define a raw cluster global test.
RawClusterCountLaneTest	This class define a raw cluster test.
RawClusterCountPooledSampleTest	The class define a test the sum on raw clusters on samples in a project.
RawClusterCountProjectTest	The class define a test the sum on raw clusters on samples in a project.
RawClusterCountSampleTest	This class define a raw clusters count test for samples.
RawClusterRecoveryCountPooledSampleTest	The class define a test the maximum on raw clusters on samples in a project.
RawClusterSDGlobalTest	This class define a raw cluster standard deviation global test.
ReadCollector	This class define a Collector for read?.xml files.
Recipe	This class define a recipe.
RecipeFinder	This class define a finder for recipe files.
RecipeFinder.RecipePath	This class define a result of the finder.
RecipeXMLParser	This class define a recipe XML parser.
RecoverablePFClusterCountSampleTest	This class define a recoverable passing filter clusters count test for samples.
RecoverablePFClusterPercentPooledSampleTest	The class define test to compute the percent recoverable passing filter clusters for a project.
RecoverablePFClusterPercentProjectTest	The class define test to compute the percent recoverable passing filter clusters for a project.
RecoverablePFClusterPercentSampleTest	This class define a recoverable passing filter clusters percent test for samples.
RecoverableRawClusterCountSampleTest	This class define a recoverable passing filter clusters count test for samples.
RecoverableRawClusterPercentPooledSampleTest	The class define test to compute the percent recoverable raw clusters for a project.
RecoverableRawClusterPercentProjectTest	The class define test to compute the percent recoverable raw clusters for a project.
RecoverableRawClusterPercentSampleTest	This class define a recoverable passing filter clusters percent test for samples.
ReDemux	This class allow to retrieve index from undetermined indices.
RSync	This class define a synchronization tool based on the rsync command.
RunConfiguration	This class define a run configuration.
RunConfigurationProvider	This interface define a run configuration provider.
RunConfigurationProviderService	This class define a service to retrieve a RunConfigurationProvider
RunData	This class define a run data.
RunData	This class define a RunData object that contains all information generated by collectors.
RunData.PooledSampleComparator	This class define a comparator to order pooled samples.
RunData.ProjectComparator	This class define a comparator to order projects.
RunDataFactory	This class define a RunData factory
RunDataGenerator	This Class collect Data.
RunDataProvider	This interface define a run data provider.
RunDataProviderService	This class define a service to retrieve a RunDataProvider
RunId	This class define a run run identifier.
RunIdGenerator	This class define an interface f that define how to create processor run data output names
RunIdStorage	This class allow to read and write processed run ids.
RunInfoCollector	This collector collect data from the RunInfo.xml file, working with all RTA versions.
RuntimePatchFastQC	This class redefine methods or constructors from FastQC to provide access to files in fastqc jar.
SampleCountGlobalTest	This class define a samples count global test.
SampleCountPooledSampleTest	The Class SampleCountSampleTest.
SampleCountProjectTest	The Class SampleCountProjectTest.
SampleInPoolCountPooledSampleTest	The class define a test giving the number of sample in a pool.
SamplesheetCollector	This class define a Bcl2fastq samplesheet collector.
SampleSheetConvertAction	This class define a sample sheet convert action.
SampleStatisticsCollector	The class define a statistic collector on sample's data to build a project summary table in qc report.
SampleTest	This interface define sample test.
ScoreInterval	This class define a score interval.
SendMail	This class is used to send emails
SequencerNames	This class allow to define names for sequencers.
SequencerSource	This class define a sequencer source.
SequencerSourceFactory	This class define a sequencer source factory.
SequencerSourceFactory.IlluminaModel	This enum defines Illumina sequencer models.
SequencerSourceFactory.Manufacturer	This enum defines sequencer manufacturers.
Settings	This class define constants to keys of configuration Aozan file.
SimpleDataTypeFilter	This class define a DataTypeFilter that require a specific DataType.
SimpleProcessResult	This class define a simple ProcessResult.
StatisticsCollector	The class define a abstract statistics collector.
StatisticsUtils	This class contains statistics methods, using the class DescriptiveStatistics from commons.apache.math.
Step	This class define a step of the recipe.
StepsXMLParser	This class define a XML parser for steps.
Storages	This class define storage for FastQ Screen.
StoragesXMLParser	This class define a XML parser for storages.
StringUtils	The Class StringUtils.
SubsetFastqCollector	This class manages the creation of subset fastq files for contamination research.
SubsetFastqThread	The class define a class for a thread that create a temporary partial fastq file, with fixed reads (200 000) to use for contamination research.
SyncDataProcessor	This class define an Illumina synchronization data processor.
Tar	This class allow to create tar files.
TechnologyDataTypeFilter	This class define a DataTypeFilter that require or not partial data..
TemplateEmailMessage	This class allow to generate EmailMessage from templates.
TestConfiguration	This class define the configuration of a test.
TestResult	This class define a test result.
TileMetricsCollector	This class collects run data by reading the TileMetricsOut.bin in InterOp directory.
UndeterminedClusterPercentGlobalTest	This class define a projects count global test.
UndeterminedIndexesCollector	This class allow to collect information about the undetermined indices that can be recovered.
UndeterminedIndexesProcessThread	This class allow to process the undetermined fastq file of a lane to extract indices that can be recovered.
UnTar	This class allow to create untar archives.
UnTar.Compression
Utils	This class contains some utility methods.
XMLUtilsParser	The class define utility methods to extract information to a xml with the good type.
XMLUtilsWriter	The class implements common action to create control quality report.
YieldLaneTest	This class define a yield lane test.
YieldPFLaneTest	This class define a yield passing filter lane test.